API for jackalope
A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
| Global functions | |
|---|---|
| add_deletion | Source code |
| add_hap_set_haps | Source code |
| add_insertion | Source code |
| add_ref_genome_chroms | Source code |
| add_ssites_cpp | Source code |
| add_substitution | Source code |
| builtin_illumina_profiles | Source code |
| check_file_existence | Source code |
| check_illumina_args | Source code |
| check_pacbio_args | Source code |
| clean_ref_genome_chrom_names | Source code |
| coal_file_sites | Source code |
| comparable | Source code |
| create_genome | Man page Source code |
| create_genome_cpp | Source code |
| create_haplotypes | Man page Source code |
| dup_hap_set_haps | Source code |
| err_msg | Source code |
| evo_rates | Man page |
| evolve_across_trees | Source code |
| examine_mutations | Source code |
| fill_coal_mat_pos | Source code |
| filter_chromosomes_cpp | Source code |
| find_profile_file | Source code |
| format_profile | Source code |
| gtrees_to_info_list | Source code |
| haplotypes | Man page |
| haps_functions | Man page |
| haps_gtrees | Man page Source code |
| haps_phylo | Man page Source code |
| haps_ssites | Man page Source code |
| haps_theta | Man page Source code |
| haps_vcf | Man page Source code |
| illumina | Man page Source code |
| illumina_hap_cpp | Source code |
| illumina_ref_cpp | Source code |
| indels | Man page Source code |
| is_type | Source code |
| jackalope | Man page |
| jackalope-package | Man page |
| make_hap_set | Source code |
| make_ref_genome | Source code |
| merge_all_chromosomes_cpp | Source code |
| merge_chromosomes_cpp | Source code |
| pacbio | Man page Source code |
| pacbio_hap_cpp | Source code |
| pacbio_ref_cpp | Source code |
| phylo_to_info_list | Source code |
| positive_vector | Source code |
| print_hap_set | Source code |
| print_ref_genome | Source code |
| process_coal_obj_sites | Source code |
| process_coal_tree_string | Source code |
| process_phy | Source code |
| rando_chroms | Source code |
| read_fasta | Man page Source code |
| read_fasta_ind | Source code |
| read_fasta_noind | Source code |
| read_ms_trees_ | Source code |
| read_profile | Source code |
| read_vcf_cpp | Source code |
| ref_genome | Man page |
| remove_hap_set_haps | Source code |
| remove_ref_genome_chroms | Source code |
| replace_Ns_cpp | Source code |
| seq_sys_by_read_length | Source code |
| set_hap_set_hap_names | Source code |
| set_ref_genome_chrom_names | Source code |
| single_integer | Source code |
| single_number | Source code |
| sub_F81 | Man page Source code |
| sub_F84 | Man page Source code |
| sub_GTR | Man page Source code |
| sub_GTR_cpp | Source code |
| sub_HKY85 | Man page Source code |
| sub_JC69 | Man page Source code |
| sub_K80 | Man page Source code |
| sub_TN93 | Man page Source code |
| sub_TN93__ | Source code |
| sub_TN93_cpp | Source code |
| sub_UNREST | Man page Source code |
| sub_UNREST_cpp | Source code |
| sub_arg_checks | Source code |
| sub_models | Man page |
| to_hap_set | Source code |
| to_hap_set__haps_gtrees_info | Source code |
| to_hap_set__haps_phylo_info | Source code |
| to_hap_set__haps_ssites_info | Source code |
| to_hap_set__haps_theta_info | Source code |
| to_hap_set__haps_vcf_info | Source code |
| trees_to_hap_set | Source code |
| using_openmp | Source code |
| view_hap_genome | Source code |
| view_hap_genome_chrom | Source code |
| view_hap_genome_chrom_sizes | Source code |
| view_hap_set_gc_content | Source code |
| view_hap_set_hap_names | Source code |
| view_hap_set_nchroms | Source code |
| view_hap_set_nhaps | Source code |
| view_hap_set_nt_content | Source code |
| view_mutations | Source code |
| view_ref_genome | Source code |
| view_ref_genome_chrom | Source code |
| view_ref_genome_chrom_names | Source code |
| view_ref_genome_chrom_sizes | Source code |
| view_ref_genome_gc_content | Source code |
| view_ref_genome_nchroms | Source code |
| view_ref_genome_nt_content | Source code |
| write_fasta | Man page Source code |
| write_gtrees | Man page Source code |
| write_haps_fasta | Source code |
| write_ref_fasta | Source code |
| write_vcf | Man page Source code |
| write_vcf_cpp | Source code |
